TerraGenome: Supporting soil metagenomics to inform soil biodiversity
Amplicon-based approaches have been used for almost a decade; however, metagenomics—and related omics-based methods—have been applied to soils during just the last five years. The promise of metagenomics is tempered by challenges associated with applying it to soil and to working with the “big data” that it generates. The goal of the TerraGenome Research Coordination Network, which is funded by the NSF, is to help overcome the challenges so that the promise can be realized. For the past three years, TerraGenome has done so by partnering with others and sponsoring sessions at meetings, working groups to identify knowledge gaps, workshops on computational approaches, and training in data analysis.
We will use examples from the literature and our own research to highlight how TerraGenome has helped scientists to develop metagenomics as a viable approach to addressing questions about how the diverse groups of microorganisms function in soils. For example, assembly of shotgun DNA sequences is fraught with difficulties, but advances in both biological and computational approaches have increased the success of assembly, in some cases even allowing for the production of draft genomes of dominant taxa. Another example related to using metagenomic information in consort with other omics methods (e.g., metatranscriptomics and metaproteomics) to achieve a more integrated understanding of the functioning biodiversity in soils.